Variant report

Variant	rs539461922
Chromosome Location	chr11:64949962-64949963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr11:64949775-64950144	MCF10A-Er-Src	breast:	n/a	chr11:64949875-64949887
2	HCFC1	chr11:64947881-64950489	Hela-S3	cervix:	n/a	n/a
3	USF1	chr11:64949711-64950152	ECC-1	luminal epithelium:	n/a	chr11:64949885-64949896
4	POLR2A	chr11:64949159-64950102	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:64948320-64950225	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:64949160-64950349	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr11:64949794-64950114	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:64949151-64950383	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr11:64949128-64950195	H1-neurons	neurons:	n/a	n/a
10	TAF1	chr11:64949739-64950180	H1-neurons	neurons:	n/a	n/a
11	MAZ	chr11:64947750-64950092	IMR90	lung:	n/a	chr11:64949232-64949242 chr11:64948375-64948385 chr11:64949219-64949229
12	CTCF	chr11:64949900-64950050	GM12873	blood:	n/a	chr11:64950006-64950019
13	MAZ	chr11:64948359-64949980	Hela-S3	cervix:	n/a	chr11:64949232-64949242 chr11:64948375-64948385 chr11:64949219-64949229
14	USF1	chr11:64949685-64950049	A549	lung:	n/a	chr11:64949885-64949896
15	TCF7L2	chr11:64949733-64950003	MCF-7	breast:	n/a	chr11:64949812-64949826
16	STAT3	chr11:64949760-64950208	MCF10A-Er-Src	breast:	n/a	chr11:64949875-64949887
17	POLR2A	chr11:64949718-64950022	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:64949718-64950017	MCF-7	breast:	n/a	n/a
19	ZNF143	chr11:64948380-64950033	H1-hESC	embryonic stem cell:	n/a	chr11:64948893-64948903 chr11:64948898-64948908 chr11:64948904-64948922
20	USF1	chr11:64949674-64950099	H1-hESC	embryonic stem cell:	n/a	chr11:64949885-64949896
21	MAX	chr11:64949660-64950033	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr11:64949817-64950052	H1-hESC	embryonic stem cell:	n/a	n/a
23	TCF7L2	chr11:64949621-64949996	Hela-S3	cervix:	n/a	chr11:64949812-64949826
24	MXI1	chr11:64949781-64950068	H1-hESC	embryonic stem cell:	n/a	chr11:64949843-64949852 chr11:64949887-64949896
25	MTA3	chr11:64949152-64950218	GM12878	blood:	n/a	n/a
26	MAX	chr11:64949641-64950126	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr11:64949840-64949980	Hela-S3	cervix:	n/a	chr11:64949843-64949852 chr11:64949887-64949896
28	USF1	chr11:64949749-64950009	A549	lung:	n/a	chr11:64949885-64949896
29	BHLHE40	chr11:64949843-64950004	K562	blood:	n/a	n/a
30	EBF1	chr11:64948422-64950064	GM12878	blood:	n/a	chr11:64948728-64948741 chr11:64949654-64949664 chr11:64949653-64949666 chr11:64948730-64948739
31	USF2	chr11:64949784-64950012	Hela-S3	cervix:	n/a	n/a
32	ZNF263	chr11:64949176-64950431	HEK293-T-REx	kidney:	n/a	n/a
33	SIN3AK20	chr11:64948257-64950383	MCF-7	breast:	n/a	n/a
34	POLR2A	chr11:64949818-64950004	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr11:64949849-64950033	MCF10A-Er-Src	breast:	n/a	chr11:64949875-64949887
36	CTCF	chr11:64949840-64949990	K562	blood:	n/a	chr11:64949894-64949902
37	POLR2A	chr11:64949147-64950320	H1-hESC	embryonic stem cell:	n/a	n/a
38	USF1	chr11:64949665-64950089	ECC-1	luminal epithelium:	n/a	chr11:64949885-64949896
39	SIN3AK20	chr11:64949381-64950084	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTBP2	chr11:64949424-64950037	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr11:64948045-64950989	K562	blood:	n/a	n/a
42	POLR2A	chr11:64948329-64950286	K562	blood:	n/a	n/a
43	MAZ	chr11:64948197-64949989	K562	blood:	n/a	chr11:64949232-64949242 chr11:64948375-64948385 chr11:64949219-64949229
44	USF1	chr11:64949763-64949962	SK-N-SH_RA	brain:	n/a	chr11:64949885-64949896
45	TBP	chr11:64949557-64950051	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr11:64949741-64949970	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr11:64948309-64950161	HUVEC	blood vessel:	n/a	n/a
48	ZBTB7A	chr11:64948082-64950057	K562	blood:	n/a	chr11:64949459-64949470
49	RCOR1	chr11:64949922-64950113	K562	blood:	n/a	n/a
50	CTCF	chr11:64949820-64949970	RPTEC	kidney:	n/a	chr11:64949894-64949902

No.	Distal block	Cell Line	Cell type
1	chr11:64897351..64905868-chr11:64946257..64954528,24	K562	blood:
2	chr11:64948280..64951360-chr11:64970311..64973843,4	MCF-7	breast:
3	chr11:64894025..64897642-chr11:64945042..64952225,7	MCF-7	breast:
4	chr11:64943825..64947169-chr11:64947454..64950649,5	K562	blood:
5	chr11:64877702..64891058-chr11:64944203..64957091,32	K562	blood:
6	chr11:64862263..64865019-chr11:64949588..64952291,3	MCF-7	breast:
7	chr11:64806998..64808499-chr11:64948414..64950755,2	MCF-7	breast:
8	chr11:64948264..64950913-chr11:64951274..64954036,3	MCF-7	breast:
9	chr11:64875868..64888016-chr11:64945810..64953962,46	MCF-7	breast:
10	chr11:64946608..64950484-chr11:65027800..65030670,5	K562	blood:
11	chr11:64947644..64950610-chr11:65027945..65030670,5	K562	blood:
12	chr11:64949731..64952366-chr11:64986911..64988700,2	K562	blood:
13	chr11:64949318..64950980-chr11:65546666..65549109,2	MCF-7	breast:
14	chr11:64900106..64905064-chr11:64945207..64950571,10	K562	blood:
15	chr11:64912371..64919818-chr11:64945990..64951836,8	MCF-7	breast:
16	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
17	chr11:64889010..64891240-chr11:64947236..64950448,4	K562	blood:
18	chr11:64888081..64892747-chr11:64946823..64951612,8	MCF-7	breast:
19	chr11:64947729..64951218-chr11:65027798..65031522,5	MCF-7	breast:
20	chr11:64778492..64782821-chr11:64947057..64951070,4	K562	blood:
21	chr11:64898025..64904360-chr11:64945543..64952640,32	MCF-7	breast:
22	chr11:64947252..64950708-chr11:65267391..65271454,4	K562	blood:
23	chr11:64646646..64648212-chr11:64949732..64952705,2	MCF-7	breast:
24	chr11:64948574..64950369-chr11:65028562..65030445,2	MCF-7	breast:
25	chr11:64946026..64951451-chr11:65265686..65269219,7	MCF-7	breast:
26	chr11:64644921..64647626-chr11:64948017..64950319,4	K562	blood:
27	chr11:64878011..64879555-chr11:64948753..64950744,2	K562	blood:

Variant related genes	Relation type
ENSG00000254614	TF binding region
CAPN1	TF binding region
ENSG00000175827	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000197847	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000222477	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000254455	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000255200	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000254470	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000168061	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv3339354	chr11:64947901-64950749	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	32 gene(s)	inside rSNPs	n/a
4	esv3437654	chr11:64948626-64950024	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64947600-64950400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:64947600-64950600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:64947600-64950800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:64947600-64951000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr11:64947800-64950200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:64947800-64950400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr11:64947800-64950600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:64947800-64952200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:64948000-64950000	Active TSS	Brain Anterior Caudate	brain
10	chr11:64948000-64950000	Active TSS	Brain Hippocampus Middle	brain
11	chr11:64948000-64950000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr11:64948000-64950000	Active TSS	Esophagus	oesophagus
13	chr11:64948000-64950000	Active TSS	Left Ventricle	heart
14	chr11:64948000-64950000	Active TSS	Pancreas	Pancrea
15	chr11:64948000-64950200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr11:64948000-64950200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:64948000-64950200	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr11:64948000-64950400	Active TSS	Brain Angular Gyrus	brain
19	chr11:64948000-64950400	Active TSS	Fetal Kidney	kidney
20	chr11:64948000-64950400	Active TSS	Right Atrium	heart
21	chr11:64948000-64950400	Active TSS	Small Intestine	intestine
22	chr11:64948000-64950600	Active TSS	NHDF-Ad	bronchial
23	chr11:64948000-64950800	Active TSS	HSMM	muscle
24	chr11:64948000-64951000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr11:64948000-64951000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:64948000-64951000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr11:64948000-64952000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr11:64948200-64950000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:64948200-64950000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:64948200-64950000	Active TSS	Primary T cells from cord blood	blood
31	chr11:64948200-64950000	Active TSS	Muscle Satellite Cultured Cells	--
32	chr11:64948200-64950000	Active TSS	Psoas Muscle	Psoas
33	chr11:64948200-64950200	Active TSS	Aorta	Aorta
34	chr11:64948200-64950200	Active TSS	Ovary	ovary
35	chr11:64948200-64950200	Active TSS	A549	lung
36	chr11:64948200-64950200	Active TSS	HSMMtube	muscle
37	chr11:64948200-64950200	Active TSS	NHLF	lung
38	chr11:64948200-64950400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:64948200-64950400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr11:64948200-64950400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:64948200-64950400	Active TSS	GM12878-XiMat	blood
42	chr11:64948200-64950800	Active TSS	Gastric	stomach
43	chr11:64948200-64951000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:64948200-64951400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr11:64948200-64951600	Enhancers	Fetal Brain Male	brain
46	chr11:64948400-64950000	Active TSS	H1 Cell Line	embryonic stem cell
47	chr11:64948400-64950000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:64948400-64950000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:64948400-64950000	Active TSS	Fetal Intestine Small	intestine
50	chr11:64948400-64950200	Active TSS	Fetal Intestine Large	intestine

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